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Detailed information for vg1218759678:

Variant ID: vg1218759678 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18759678
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGATGTCACGTGGCTTGCAACGCAGCACCATGTCCGAGGTGACGAAGTTCTCCTCGGCAGCGACAGACGCGATGAACTCGAGGACCACGTCGTGCACCTT[C/A]
ACCTTCACGACGTCCCCCGCCTCCACCGGCTGGATCAGCTGTCGGTTGACGAGCTCGTTGAAGTAGCTCTCGGCCGTCTCCCATAACGTGACCTGCTCCT

Reverse complement sequence

AGGAGCAGGTCACGTTATGGGAGACGGCCGAGAGCTACTTCAACGAGCTCGTCAACCGACAGCTGATCCAGCCGGTGGAGGCGGGGGACGTCGTGAAGGT[G/T]
AAGGTGCACGACGTGGTCCTCGAGTTCATCGCGTCTGTCGCTGCCGAGGAGAACTTCGTCACCTCGGACATGGTGCTGCGTTGCAAGCCACGTGACATCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.50% 1.70% 0.44% 1.31% NA
All Indica  2759 97.50% 2.40% 0.11% 0.00% NA
All Japonica  1512 94.40% 0.50% 1.06% 4.10% NA
Aus  269 98.90% 0.40% 0.74% 0.00% NA
Indica I  595 98.70% 1.00% 0.34% 0.00% NA
Indica II  465 98.70% 1.10% 0.22% 0.00% NA
Indica III  913 96.40% 3.60% 0.00% 0.00% NA
Indica Intermediate  786 97.20% 2.80% 0.00% 0.00% NA
Temperate Japonica  767 90.60% 0.00% 1.96% 7.43% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 2.90% 0.41% 2.07% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1218759678 C -> DEL LOC_Os12g31160.1 N frameshift_variant Average:71.092; most accessible tissue: Zhenshan97 young leaf, score: 88.759 N N N N
vg1218759678 C -> A LOC_Os12g31160.1 synonymous_variant ; p.Val489Val; LOW synonymous_codon Average:71.092; most accessible tissue: Zhenshan97 young leaf, score: 88.759 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218759678 NA 1.31E-06 mr1094 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218759678 NA 5.37E-07 mr1242 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218759678 NA 3.66E-09 mr1458 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218759678 NA 6.42E-06 mr1121_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218759678 NA 4.92E-06 mr1123_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218759678 NA 2.18E-06 mr1242_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218759678 NA 1.00E-10 mr1458_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1218759678 4.85E-06 5.45E-07 mr1932_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251